Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates.

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Mitogen-activated protein kinase (MAPK) cascades are one of the signaling modules that mediate transduction of extracellular microbial signals into appropriate cellular responses. Here, we employ a transgenic system that simulates activation of two pathogen/stress-responsive MAPKs to study release of metabolites and proteins into root exudates. The premise is based on our previous proteomics study that suggests upregulation of secretory processes in this transgenic system. An advantage of this experimental set-up is the direct focus on MAPK-regulated processes without the confounding complications of other signaling pathways activated by exposure to microbes or microbial molecules. Using non-targeted metabolomics and proteomics studies, we show that MAPK activation can indeed drive the appearance of dipeptides, defense-related metabolites and proteins in root apoplastic fluid. However, the relative levels of other compounds in the exudates were decreased. This points to a bidirectional control of metabolite and protein release into the apoplast. The putative roles for some of the identified apoplastic metabolites and proteins are discussed with respect to possible antimicrobial/defense or allelopathic properties. Overall, our findings demonstrate that sustained activation of MAPKs alters the composition of apoplastic root metabolites and proteins, presumably to influence the plant-microbe interactions in the rhizosphere. The reported metabolomics and proteomics data are available via Metabolights (Identifier: MTBLS441) and ProteomeXchange (Identifier: PXD006328), respectively.", "claims": [{"id": "claim-method", "statement": "ANOVA applying a permutation based FDR threshold (250 randomizations) of 5% was performed and the abundance of proteins with q-values below said α = 0.05 were considered to change significantly between the groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28785276", "locator": "sections[8] \"Proteome analysis of root exudates\" paragraph 4", "quote": "ANOVA applying a permutation based FDR threshold (250 randomizations) of 5% was performed and the abundance of proteins with q-values below said α = 0.05 were considered to change significantly between the groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Metabolomics data is available in the Metabolights repository under the accession number (MTBLS441, http://www.ebi.ac.uk/metabolights/MTBLS441). 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The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD006328 and DOI 10.6019/PXD006328."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Non-targeted metabolomics and proteomics showed that sustained MAPK activation altered the composition of apoplastic root metabolites and proteins; the underlying data are available through Metabolights (MTBLS441) and ProteomeXchange (PXD006328).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28785276", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using non-targeted metabolomics and proteomics studies, we show that MAPK activation can indeed drive the appearance of dipeptides, defense-related metabolites and proteins in root apoplastic fluid."}, {"asset": "source:pmid:28785276", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Overall, our findings demonstrate that sustained activation of MAPKs alters the composition of apoplastic root metabolites and proteins, presumably to influence the plant-microbe interactions in the rhizosphere."}, {"asset": "source:pmid:28785276", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The reported metabolomics and proteomics data are available via Metabolights (Identifier: MTBLS441) and ProteomeXchange (Identifier: PXD006328), respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Non-targeted metabolomics and proteomics showed that sustained MAPK activation altered the composition of apoplastic root metabolites and proteins; the underlying data are available through Metabolights (MTBLS441) and ProteomeXchange (PXD006328).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28785276"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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Nguyen-Kim et al., 2016"], ["AT5G19860", "Protein of unknown function, DUF538", "Extracellular", "Nguyen-Kim et al., 2016"], ["AT5G23840", "MD-2-related lipid recognition domain-containing protein", "PM/extracellular", "predicted by SUBA"], ["AT1G72160", "Sec 14p-like phosphatidylinositol transfer family protein", "PM", "De Michele et al., 2016"], ["AT2G45820", "Remorin family protein", "PM", "De Michele et al., 2016"], ["AT3G01290", "Hypersensitive induced reaction (HIR2) proteins", "PM", "De Michele et al., 2016"], ["AT2G23120", "Group 6 LEA (Late embryogenesis abundant) protein", "PM", "De Michele et al., 2016"], ["AT2G24940", "Membrane-associated progesterone binding protein 2, MAPR2", "PM", "De Michele et al., 2016"], ["AT4G23470", "PLAC8 family protein", "PM/vacuole membrane", "Mitra et al., 2009"], ["AT5G54500", "FQR1 (flavodoxin-like quinone reductase 1)", "PM/extracellular", "deDe Michele et al., 2016"], ["AT4G38510", "ATPase, V1 complex, subunit B protein", "PM", "Heard et al., 2015; De Michele et al., 2016"], ["AT1G76030", "ATPase, V1 complex, subunit B protein", "PM", "Heard et al., 2015; De Michele et al., 2016"], ["AT2G43910", "HOL1 (HARMLESS TO OZONE LAYER 1)", "PM", "De Michele et al., 2016"], ["AT5G41950", "Tetratricopeptide repeat (TPR)-like superfamily protein", "PM/Golgi", "Zhang and Peck, 2011"], ["AT5G11670", "NADP-malic enzyme 2", "Plastids/PM", "Helm et al., 2014; De Michele et al., 2016"], ["AT1G62480", "Vacuolar calcium-binding protein-related", "Plastids/PM", "De Michele et al., 2016"], ["AT3G13300", "Varicose, Transducin/WD40 repeat-like superfamily protein", "Cytoplasm, P-body/PM", "Zhang and Peck, 2011"], ["AT1G08880", "HTA5, γ-H2AX, Histone superfamily protein", "Nucleus/PM/extracellular", "Mitra et al., 2009; Nguyen-Kim et al., 2016"], ["AT5G59870", "HTA6, Histone H2A 6", "Nucleus/extracellular", "Nguyen-Kim et al., 2016"], ["AT1G51060", "HTA10, Histone H2A 10", "Nucleus/extracellular", "Nguyen-Kim et al., 2016"], ["AT1G52740", "HTA9, Histone H2A protein 9", "Nucleus/multivesicular body", "Heard et al., 2015"], ["AT3G20670", "HTA13, Histone H2A 13", "Nucleus/extracellular", "Nguyen-Kim et al., 2016"], ["AT1G21120", "IGMT2, Indole Glucosinolate O-methyltransferase 2", "Cytosol", "predicted by AmiGO"], ["AT1G21130", "IGMT4, Indole Glucosinolate O-methyltransferase 4", "Cytosol", "predicted by AmiGO"], ["AT5G16390", "Chloroplastic acetylcoenzyme A carboxylase 1", "Chloroplast", "Melonek et al., 2016"]], "row_count": 30, "column_count": 4, "numeric_cells": 75, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:PXD006328 not downloaded", "asset:data:geo:PXD006328 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "ANOVA applying a permutation based FDR threshold (250 randomizations) of 5% was performed and the abundance of proteins with q-values below said α = 0.05 were considered to change significantly between the groups."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}, {"id": "method-4", "family": "clustering", "specific": "kmeans", "label": "Clustering", "dsl_operations": ["kmeans_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "k-means"}}, {"id": "method-5", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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